rs9314832

Variant names:

• chr9-75368285-G-A
• rs9314832

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.126 in 152,156 control chromosomes in the GnomAD database, including 1,489 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1489 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19155 AN: 152038 Hom.: 1487 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.109

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.126 AC: 19189 AN: 152156 Hom.: 1489 Cov.: 33 AF XY: 0.125 AC XY: 9283 AN XY: 74384

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0365

Gnomad4 NFE AF: 0.0861

Gnomad4 OTH AF: 0.115

Alfa AF: 0.120 Hom.: 223

Bravo AF: 0.134

Asia WGS AF: 0.142 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9314832; hg19: chr9-77983201;